RetrogeneDB ID: retro_fcat_960

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:53810968..53811461(+)
• Located in intron of: ENSFCAG00000000247

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000002503
• Aliases: None
• Description: None

Sequence

>retro_fcat_960
ACTCTCCTAGGTTGCAGACAGGCTAGGCTGACTGGTGTTCCGACTTGTAAACTTGGGATTGAAACTTAATAAAATCGACC
ATTCCTCCATGACCCACGCGATAGAAACCACTGACATCGTCAGCAAACACGTGCCAGGGGTCTGCAAAGTCAGCACAGAC
CTGCTGAGGGAAGGCGCCCATATCTAGCTGAACGAGCTGAATAGGCCCAAGTCGCACTGGAAGCCCGAAACTGAGGGTAT
TAGGAAGACAGAGCCGGAAGGGAAGTGGCTTACTAAATTGCATCCACCTGGCAGACGCCAGGCAGCAGAATGGTTCTGAA
ATCTGCCATGCCACCTTTTGCAACCTGATGTGTCCGGCGCCAGAGTTCTTTCAGAAGGCTGGCTCCGCCTCTCCCTCAAC
AACCGCAGCATTATCCAGCTGGTGGTCTCGTCTAGTTGCAGAGTAGCGCTCAGGGTCCTCAGAGACATAGGGTTCAGGCC
TCCTGATAAGATC

Alignment

ORF - retro_fcat_960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.27 %
• Parental protein coverage: 63.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TPLGREQAELTGL-RLASLGLKFNKIVHSSMTRAIETTDIISKHLPGVSKVSTDLLREGAPI---EPDPP
          T.LG..QA.LTG..RL..LGLK.NKI.HSSMT.AIETTDI.SKH.PGV.KVSTDLLREGA.I...E...P
Retrocopy TLLGCRQARLTGV>RLVNLGLKLNKIDHSSMTHAIETTDIVSKHVPGVCKVSTDLLREGAHI*LNELNRP

Parental  VSHWKPEAV-QYYEDGARIEAAF-RNYIHRADAKQQEDSYEIFICHANVIRYIVCRALQF-PPEGWLRLS
          .SHWKPE....Y.ED.A..E.A...N.IH.ADA.QQ..S....ICHA.......C.A..F...EGWLRLS
Retrocopy KSHWKPETE<GY*EDRAGREVAY<LNCIHLADARQQNGSE---ICHATFCN-LMCPAPEF<LSEGWLRLS

Parental  LNNGSITHLVVRPDGRVALRALGDTGFMPPDKI
          LNN.SI..LVV....RVALR.L.D.GF.PPDKI
Retrocopy LNNRSIIQLVVSSSCRVALRVLRDIGFRPPDKI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	7.23 RPM
SRP017611_kidney	0.00 RPM	9.69 RPM
SRP017611_liver	0.00 RPM	4.45 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_960 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_960 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013437	2 retrocopies	retro_amel_1052, retro_amel_173,
Choloepus hoffmanni	ENSCHOG00000011867	2 retrocopies	retro_chof_1762, retro_chof_2590,
Felis catus	ENSFCAG00000002503	2 retrocopies	retro_fcat_800, retro_fcat_960 ,
Homo sapiens	ENSG00000247077	1 retrocopy	retro_hsap_3363,
Myotis lucifugus	ENSMLUG00000013646	1 retrocopy	retro_mluc_1270,
Macaca mulatta	ENSMMUG00000015466	1 retrocopy	retro_mmul_2101,
Mustela putorius furo	ENSMPUG00000002639	1 retrocopy	retro_mputfur_684,
Pan troglodytes	ENSPTRG00000005657	1 retrocopy	retro_ptro_2286,
Rattus norvegicus	ENSRNOG00000037443	1 retrocopy	retro_rnor_1597,
Sus scrofa	ENSSSCG00000026764	1 retrocopy	retro_sscr_821,
Tursiops truncatus	ENSTTRG00000010653	1 retrocopy	retro_ttru_208,